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debug of Wolman computation + not fitted grains are exported in results (used in Python and Matlab)

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This commit is contained in:
Paul Leroy
2025-03-28 17:06:10 +01:00
parent eafc4c80bf
commit 0982fd942d
5 changed files with 112 additions and 43 deletions
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CMakeLists.txt
+1 -1
View File
@@ -16,7 +16,7 @@ target_sources(G3PointPlugin
ui/WolmanCustomPlot.ui
)
set(QG3POINT_PLUGIN_VERSION "0.5")
set(QG3POINT_PLUGIN_VERSION "0.6")
add_subdirectory( include )
add_subdirectory( src )
src/G3PointAction.cpp
+52 -13
View File
@@ -1135,7 +1135,7 @@ bool G3PointAction::wolman()
ellipsoidLabels(i) = i;
}
// rebuild a matrix with the coordinates the labels of the original cloud
// rebuild vectors with the coordinates and the labels of the original points
int n_points = m_grainsAsEllipsoids->m_cloud->size();
Eigen::ArrayXf x(n_points);
Eigen::ArrayXf y(n_points);
@@ -1178,13 +1178,17 @@ bool G3PointAction::wolman()
Eigen::ArrayXf distances;
Eigen::Index minLoc;
if (k % 20 == 0)
if (k % 20 == 0) // display progress
{
std::cout << k << std::endl;
}
float r0 = dist(urbg);
float r1 = dist(urbg);
// std::cout << r0 << ", " << r1 << "," << std::endl;
// #pragma omp critical
// {
// std::cout << r0 << ", " << r1 << "," << std::endl;
// }
x_grid = arange(x.minCoeff() - r0 * dx, x.maxCoeff(), dx);
y_grid = arange(y.minCoeff() - r1 * dx, y.maxCoeff(), dx);
int nx = x_grid.size();
@@ -1200,36 +1204,57 @@ bool G3PointAction::wolman()
iWolman(ix, iy) = minLoc;
}
}
// std::cout << dist.block(0, 0, 5, 5) << std::endl;
// std::cout << iWolman.block(0, 0, 5, 5) << std::endl;
XXb condition = (dist < dx / 10);
Eigen::ArrayXf iWolmanSelection(condition.count());
int indexInWolmanSelection = 0;
for (int k = 0; k < condition.size(); k++)
// for (int k = 0; k < condition.size(); k++)
// {
// if (condition(k))
// {
// iWolmanSelection(indexInWolmanSelection) = iWolman(k);
// indexInWolmanSelection++;
// }
// }
for (int ix = 0; ix < nx; ix++)
{
if (condition(k))
for (int iy = 0; iy < ny; iy++)
{
iWolmanSelection(indexInWolmanSelection) = iWolman(k);
indexInWolmanSelection++;
if (condition(ix, iy))
{
iWolmanSelection(indexInWolmanSelection) = iWolman(ix, iy);
indexInWolmanSelection++;
}
}
}
Eigen::ArrayXi wolmanSelection;
wolmanSelection = pointsLabels(iWolmanSelection);
// std::cout << "[" << k << "] wolmanSelection\n" << wolmanSelection << std::endl;
std::unordered_set<int> setOfA(wolmanSelection.begin(), wolmanSelection.end());
std::vector<int> y_ind;
// // A is wolmanSelection
// // B is ellipsoidsLabels
for (int i = 0; i < nEllipsoids; ++i)
for (auto label : wolmanSelection)
{
int ellipsoidLabel = ellipsoidLabels[i];
if (setOfA.find(ellipsoidLabel) != setOfA.end())
// some grains does not have an associated ellipdsoid, they shall not be considered in the Wolman statistics
if (m_grainsAsEllipsoids->m_fitNotOK.count(label))
{
y_ind.push_back(ellipsoidLabel);
// std::cout << "discard ellipsoid with label: "<< ellipsoidLabel << " (fitNotOK)" << std::endl;
continue;
}
else
{
y_ind.push_back(label);
}
}
Eigen::ArrayXf d_item(y_ind.size());
// std::cout << "y_ind\n";
for (int i = 0; i < y_ind.size(); i++)
{
// std::cout << y_ind[i] << " " ;
d_item(i) = b_axis(y_ind[i]) * 1000; // conversion to mm
}
// std::cout << std::endl;
// std::cout << "[" << k << "] " << d_item << std::endl;
#pragma omp critical
{
d.push_back(d_item);
@@ -1247,6 +1272,8 @@ bool G3PointAction::wolman()
dq(i, Eigen::all) << quant(d[i], 0.1), quant(d[i], 0.5), quant(d[i], 0.9);
}
// std::cout << "d_sample " << d_sample << std::endl;
// compute standard deviation
Eigen::Array3d edq {std_dev(dq(Eigen::all, 0)),
std_dev(dq(Eigen::all, 1)),
@@ -1255,6 +1282,18 @@ bool G3PointAction::wolman()
quant(d_sample, 0.5),
quant(d_sample, 0.9)};
// std::cout << "d_sample\n" << d_sample << std::endl;
std::cout << "quantl 0.1 0.5 0.9 \n"
<< dq_final(0) << " "
<< dq_final(1) << " "
<< dq_final(2) << std::endl;
std::cout << "std_dev 0.1 0.5 0.9 \n"
<< edq(0) << " "
<< edq(1) << " "
<< edq(2) << std::endl;
showWolman(d_sample, dq_final, edq);
return true;
src/G3PointPlots.cpp
+2 -2
View File
@@ -89,9 +89,9 @@ bool G3PointPlots::exportToCSV(QString filename, SharedDataContainer container,
if (dq_final) // WolmanCustomPlot
{
stream << "# D10 [mm], D50 [mm], D90 [mm]" << endl;
stream << (*dq_final)(0) << (*dq_final)(0) << (*dq_final)(0) << endl;
stream << (*dq_final)(0) << " " << (*dq_final)(1) << " " << (*dq_final)(2) << endl;
stream << "# std(D10) [mm], std(D50) [mm], std(D90) [mm]" << endl;
stream << (*edq)(0) << (*edq)(0) << (*edq)(0) << endl;
stream << (*edq)(0) << " " << (*edq)(1) << " " << (*edq)(2 ) << endl;
stream << "diameter [m], pdf" << endl;
}
else // AnglesCustomPlot
src/GrainsAsEllipsoids.cpp
+34 -22
View File
@@ -74,11 +74,25 @@ GrainsAsEllipsoids::GrainsAsEllipsoids(ccPointCloud *cloud, ccMainAppInterface *
}
// remove data corresponding to stacks were the fit was not successful
Eigen::Array3f nullArray;
nullArray.fill(NAN);
for (auto el : m_fitNotOK)
{
m_center[el] = nullArray;
// if the fit is not OK, we use the centroid as a center
int nPoints = m_stacks[el].size();
Eigen::MatrixX3d points(nPoints, 3);
for (int index = 0; index < nPoints; index++)
{
const CCVector3* point = m_cloud->getPoint(m_stacks[el][index]);
points(index, 0) = point->x;
points(index, 1) = point->y;
points(index, 2) = point->z;
}
// compute the centroid of the label
Eigen::RowVector3d centroid = points.colwise().mean();
m_center[el] << centroid.x(), centroid.y(), centroid.z();
m_radii[el].fill(0);
m_rotationMatrix[el].fill(NAN);
}
m_ccBBoxAll.setValidity(true);
@@ -113,10 +127,10 @@ bool GrainsAsEllipsoids::exportResultsAsCloud()
for (int idx = 0; idx < m_center.size(); idx++)
{
if (m_fitNotOK.count(idx))
{
continue;
}
// if (m_fitNotOK.count(idx))
// {
// continue;
// }
Eigen::Vector3f center {m_center[idx].x(), m_center[idx].y(), m_center[idx].z()};
Eigen::Vector3f point = center;
CCVector3 ccPoint(point(0), point(1), point(2));
@@ -149,10 +163,10 @@ bool GrainsAsEllipsoids::exportResultsAsCloud()
int indexInResults = 0;
for (int index = 0; index < m_center.size(); index++)
{
if (m_fitNotOK.count(index)) // when the fit was not successful, the point is not exported
{
continue;
}
// if (m_fitNotOK.count(index)) // when the fit was not successful, the point is not exported
// {
// continue;
// }
sf->setValue(indexInResults, index);
indexInResults++;
}
@@ -172,10 +186,10 @@ bool GrainsAsEllipsoids::exportResultsAsCloud()
CCCoreLib::ScalarField* sfRadiusZ = cloud->getScalarField(sfIdxRadiusZ);
for (unsigned int index = 0; index < cloud->size(); index++)
{
if (m_fitNotOK.count(index))
{
continue;
}
// if (m_fitNotOK.count(index))
// {
// continue;
// }
sfRadiusX->setValue(index, m_radii[index].x());
sfRadiusY->setValue(index, m_radii[index].y());
sfRadiusZ->setValue(index, m_radii[index].z());
@@ -213,10 +227,10 @@ bool GrainsAsEllipsoids::exportResultsAsCloud()
CCCoreLib::ScalarField* sfR22 = cloud->getScalarField(sfIdxR22);
for (unsigned int index = 0; index < cloud->size(); index++)
{
if (m_fitNotOK.count(index))
{
continue;
}
// if (m_fitNotOK.count(index))
// {
// continue;
// }
sfR00->setValue(index, m_rotationMatrix[index](0, 0));
sfR01->setValue(index, m_rotationMatrix[index](0, 1));
sfR02->setValue(index, m_rotationMatrix[index](0, 2));
@@ -241,8 +255,6 @@ bool GrainsAsEllipsoids::exportResultsAsCloud()
cloud->showColors(true);
cloud->setPointSize(9);
// m_cloud->getParent()->addChild(cloud, ccHObject::DP_PARENT_OF_OTHER, 0);
// m_app->addToDB(cloud);
m_cloud->addChild(cloud);
m_app->addToDB(cloud);
@@ -1250,7 +1262,7 @@ bool GrainsAsEllipsoids::fromFile_MeOnly(QFile& in, short dataVersion, int flags
{
float maxRadius = m_radii[idx].maxCoeff();
CCVector3 center(m_center[idx](0), m_center[idx](1), m_center[idx](2));
if (center.x != center.x)
if (m_radii[idx].x() != -1) // all radii are equal to zero when the fit was not successful
{
m_fitNotOK.insert(idx);
continue;
src/WolmanCustomPlot.cpp
+23 -5
View File
@@ -1,6 +1,8 @@
#include "WolmanCustomPlot.h"
#include "ui_WolmanCustomPlot.h"
#include <iostream>
WolmanCustomPlot::WolmanCustomPlot(const Eigen::ArrayXf &d_sample, const Eigen::Array3d& dq_final, const Eigen::Array3d& edq):
m_dq_final(dq_final),
m_edq(edq),
@@ -15,14 +17,30 @@ WolmanCustomPlot::WolmanCustomPlot(const Eigen::ArrayXf &d_sample, const Eigen::
QPen pen;
m_graph = this->addGraph();
QVector<double> x_data(d_sample.size());
QVector<double> y_data(d_sample.size());
for (int k = 0; k < d_sample.size(); k++)
// build x_data
int nSamples = d_sample.size();
QVector<double> x_data(nSamples);
for (int k = 0; k < nSamples; k++)
{
x_data[k] = d_sample(k);
y_data[k] = (static_cast<double>(k)) / static_cast<double>(d_sample.size());
}
std::sort(x_data.begin(), x_data.end());
while(x_data.contains(0.))
{
int index = x_data.indexOf(0.);
std::cout << "[WolmanCustomPlot::WolmanCustomPlot] remove null diameter at index " << QString::number(index).toStdString() << std::endl;
x_data.remove(index);
}
std::sort(x_data.begin(), x_data.end()); // sort diameters
// build y_data
int nValidSamples = x_data.size();
QVector<double> y_data(nValidSamples);
for (int k = 0; k < nValidSamples; k++)
{
y_data[k] = (static_cast<double>(k)) / static_cast<double>(nValidSamples);
}
m_graph->setData(x_data, y_data);
m_graph->rescaleAxes();
// give the axes some labels: